Halo 2 Walkthrough
Off the Rock, Through the Bush, Nothing but Jackal
This is a HUGE map area and can get very confusing. Really your aim here is just to slay everyone before you can do anything else. So go up the stream, down the stream, onto all of the ledges until everyone is dead. There's a dark tunnel but it doesn't lead anywhere, it just has some weapons in it. Go into every nook and cranny to find the remaining enemies. When you get them all, you'll get a checkpoint.

Now you're told you have to go to the island. Go up as high as you can, working your way around to where the metal pod / containers are, that the enemy was sniping you from. If you wait long enough you'll get a marker leading you to here. You head down a narrow pathway back to the lake with the temple in it.

Cortana says that the Covenant doens't think we're a threat, checkpoint. Go down onto the balcony area and then forward to the building. You go through a pair of doors, checkpoint.

This is a rough fight so be ready. There are 5-6 elite honor guards in here who can kill you pretty much with one blow. Stay in the doorway area and snipe them, throwing grenades when they try to come near you. Once you get your hands on a sword, you can kill them with one blow. Once they're all dead, Cortana says "wait, go back" - she wants to see the hologram of the prophet.

Apparently he's planning on activating Halo. She turns his language into English and you hear "burn a path into the divine beyond". She and the ship's captain talk and decide that the prophet would need the item from the library just as with the other Halo. The captain will go take on the library, it's your job to kill off the prophet.